Scanning transmission electron microscopy (STEM) has been applied to determine the subunit organization of the ATP-dependent protease, Lon. This enzyme plays an important role in degrading misfolded proteins in prokaryotes as well as in the mitochrondria of eukaryotes. Lon consists of multiple copies of a single polypeptide chain that contains both the ATPase (A) and protease (P) domains. The sequence of bacterial Lon has a strong homology with eukaryotic Lon which has been reported to form heptameric rings. However, for bacterial Lon, currently published data are inconclusive. Dark-field STEM measurements show that full-length E. coli Lon (wild type and a ser-ala mutant) as well as Lon-NA are composed of dodecamers, whereas Lon-AP forms hexamers. By analogy with the protein ClpA which is the ATPase component of the ClpAP protease complex, it is likely that Lon is comprised of two hexameric rings. The fact that Lon-AP only forms hexamers suggests that the N-terminal domain may be required for association of two hexameric rings in the holoenzyme. - Scanning transmission electron microscopy, lon protease, subunit organization, structure, molecular weight